bdext 0.1.65__py3-none-any.whl → 0.1.67__py3-none-any.whl

bdext-0.1.65.dist-info/METADATA

@@ -1,178 +0,0 @@
-Metadata-Version: 2.1
-Name: bdext
-Version: 0.1.65
-Summary: Estimation of BDEISS-CT parameters from phylogenetic trees.
-Home-page: https://github.com/modpath/bdeissct
-Author: Anna Zhukova
-Author-email: anna.zhukova@pasteur.fr
-License: UNKNOWN
-Keywords: phylogenetics,birth-death model,incubation,super-spreading,contact tracing
-Platform: UNKNOWN
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Developers
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Software Development
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Description-Content-Type: text/markdown
-Requires-Dist: tensorflow==2.19.0
-Requires-Dist: six
-Requires-Dist: ete3
-Requires-Dist: numpy==2.0.2
-Requires-Dist: scipy==1.14.1
-Requires-Dist: biopython
-Requires-Dist: scikit-learn==1.5.2
-Requires-Dist: pandas==2.2.3
-Requires-Dist: treesumstats==0.7
-
-# bdeissct_dl
-
-Estimator of BDEISS-CT model parameters from phylogenetic trees 
-
-
-
-[//]: # ([![DOI:10.1093/sysbio/syad059](https://zenodo.org/badge/DOI/10.1093/sysbio/syad059.svg)](https://doi.org/10.1093/sysbio/syad059))
-[![GitHub release](https://img.shields.io/github/v/release/evolbioinfo/bdeissct_dl.svg)](https://github.com/evolbioinfo/bdeissct_dl/releases)
-[![PyPI version](https://badge.fury.io/py/bdeissct_dl.svg)](https://pypi.org/project/bdeissct_dl/)
-[![PyPI downloads](https://shields.io/pypi/dm/bdeissct_dl)](https://pypi.org/project/bdeissct_dl/)
-[![Docker pulls](https://img.shields.io/docker/pulls/evolbioinfo/bdeissct)](https://hub.docker.com/r/evolbioinfo/bdeissct/tags)
-
-## BDEISS-CT model
-
-BD-PN model extends the classical birth-death (BD) model with incomplete sampling [[Stadler 2009]](https://pubmed.ncbi.nlm.nih.gov/19631666/), by adding partner notification (PN).
-Under this model, infected individuals can transmit their pathogen with a constant rate λ, 
-get removed (become non-infectious) with a constant rate ψ, 
-and their pathogen can be sampled upon removal 
-with a constant probability ρ. On top of that, in the BD-PN model, 
-at the moment of sampling the sampled individual 
-might notify their most recent partner with a constant probability υ. 
-Upon notification, the partner is removed almost instantaneously (modeled via a constant notified
-removal rate φ >> ψ) and their pathogen is sampled.
-
-BD-PN model therefore has 5 parameters:
-* λ -- transmission rate
-* ψ -- removal rate
-* ρ -- sampling probability upon removal
-* υ -- probability to notify the last partner upon sampling
-* φ -- removal (and sampling) rate after notification
-
-These parameters can be expressed in terms of the following epidemiological parameters:
-* R<sub>0</sub>=λ/ψ -- reproduction number
-* 1/ψ -- infectious time
-* 1/φ -- partner removal time
-
-BD-CT model makes 3 assumptions:
-1. only observed individuals can notify (instead of any removed individual);
-2. notified individuals are always observed upon removal;
-3. only the most recent partner can get notified.
-
-For identifiability, BD-PN model requires one of the three BD model parameters (λ, ψ, ρ) to be fixed.
-
-## BDEISS-CT parameter estimator
-
-The bdeissct_dl package provides deep-learning-based BDEISS-CT model parameter estimator 
-from a user-supplied time-scaled phylogenetic tree. 
-User must also provide a value for one of the three BD model parameters (λ, ψ, or ρ). 
-We recommend providing the sampling probability ρ, 
-which could be estimated as the number of tree tips divided by the number of declared cases for the same time period.
-
-
-## Input data
-One needs to supply a time-scaled phylogenetic tree in newick format. 
-In the examples below we will use an HIV tree reconstructed from 200 sequences, 
-published in [[Rasmussen _et al._ PLoS Comput. Biol. 2017]](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005448), 
-which you can find at [PairTree GitHub](https://github.com/davidrasm/PairTree) 
-and in [hiv_zurich/Zurich.nwk](hiv_zurich/Zurich.nwk). 
-
-## Installation
-
-There are 4 alternative ways to run __bdeissct_dl__ on your computer: 
-with [docker](https://www.docker.com/community-edition), 
-[apptainer](https://apptainer.org/),
-in Python3, or via command line (requires installation with Python3).
-
-
-
-### Run in python3 or command-line (for linux systems, recommended Ubuntu 21 or newer versions)
-
-You could either install python (version 3.9 or higher) system-wide and then install bdeissct_dl via pip:
-```bash
-sudo apt install -y python3 python3-pip python3-setuptools python3-distutils
-pip3 install bdeissct_dl
-```
-
-or alternatively, you could install python (version 3.9 or higher) and bdeissct_dl via [conda](https://conda.io/docs/) (make sure that conda is installed first). 
-Here we will create a conda environment called _phyloenv_:
-```bash
-conda create --name phyloenv python=3.12
-conda activate phyloenv
-pip install bdeissct_dl
-```
-
-
-#### Basic usage in a command line
-If you installed __bdeissct_dl__ in a conda environment (here named _phyloenv_), do not forget to first activate it, e.g.
-
-```bash
-conda activate phyloenv
-```
-
-Run the following command to estimate the BDEISS_CT parameters and their 95% CIs for this tree, assuming the sampling probability of 0.25, 
-and save the estimated parameters to a comma-separated file estimates.csv.
-```bash
-bdeissct_infer --nwk Zurich.nwk --ci --p 0.25 --log estimates.csv
-```
-
-#### Help
-
-To see detailed options, run:
-```bash
-bdeissct_infer --help
-```
-
-
-### Run with docker
-
-#### Basic usage
-Once [docker](https://www.docker.com/community-edition) is installed, 
-run the following command to estimate BDEISS-CT model parameters:
-```bash
-docker run -v <path_to_the_folder_containing_the_tree>:/data:rw -t evolbioinfo/bdeissct --nwk /data/Zurich.nwk --ci --p 0.25 --log /data/estimates.csv
-```
-
-This will produce a comma-separated file estimates.csv in the <path_to_the_folder_containing_the_tree> folder,
- containing the estimated parameter values and their 95% CIs (can be viewed with a text editor, Excel or Libre Office Calc).
-
-#### Help
-
-To see advanced options, run
-```bash
-docker run -t evolbioinfo/bdeissct -h
-```
-
-
-
-### Run with apptainer
-
-#### Basic usage
-Once [apptainer](https://apptainer.org/docs/user/latest/quick_start.html#installation) is installed, 
-run the following command to estimate BDEISS-CT model parameters (from the folder where the Zurich.nwk tree is contained):
-
-```bash
-apptainer run docker://evolbioinfo/bdeissct --nwk Zurich.nwk --ci --p 0.25 --log estimates.csv
-```
-
-This will produce a comma-separated file estimates.csv,
- containing the estimated parameter values and their 95% CIs (can be viewed with a text editor, Excel or Libre Office Calc).
-
-
-#### Help
-
-To see advanced options, run
-```bash
-apptainer run docker://evolbioinfo/bdeissct -h
-```
-
-
-
-

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